group autoannotation and consensus display settings

[jalview.git] / src / jalview / gui / Preferences.java

diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index 6d94687..6273fbc 100755 (executable)
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -84,9 +84,8 @@ public class Preferences extends GPreferences
      */
     
     groupURLLinks = new Vector();
-    groupURLLinks.addElement("UNIPROT|EnVision2|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?workflow=Default&datasetName=JalviewIDs$DATASETID$&input=$SEQUENCEIDS$&inputType=0|,");
-    // TODO: make sequence Group URL links more efficiently generated so popup menu does not take so long. 
-    // groupURLLinks.addElement("Seqs|EnVision2|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?workflow=Default&datasetName=JalviewSeqs$DATASETID$&input=$SEQUENCES=/([A-Za-z]+)+/=$&inputType=1|,");
+    groupURLLinks.addElement("UNIPROT|EnVision2|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?tool=Jalview&workflow=Default&datasetName=JalviewIDs$DATASETID$&input=$SEQUENCEIDS$&inputType=0|,");
+    groupURLLinks.addElement("Seqs|EnVision2|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?tool=Jalview&workflow=Default&datasetName=JalviewSeqs$DATASETID$&input=$SEQUENCES=/([A-Za-z]+)+/=$&inputType=1|,");
     
   }
 
@@ -122,10 +121,6 @@ public class Preferences extends GPreferences
     fullScreen.setSelected(Cache.getDefault("SHOW_FULLSCREEN", false));
     annotations.setSelected(Cache.getDefault("SHOW_ANNOTATIONS", true));
 
-    conservation.setEnabled(Cache.getDefault("SHOW_ANNOTATIONS", true));
-    quality.setEnabled(Cache.getDefault("SHOW_ANNOTATIONS", true));
-    identity.setEnabled(Cache.getDefault("SHOW_ANNOTATIONS", true));
-
     conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));
     quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));
     identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
@@ -202,6 +197,11 @@ public class Preferences extends GPreferences
 
     autoCalculateConsCheck.setSelected(Cache.getDefault(
             "AUTO_CALC_CONSENSUS", true));
+    showGroupConsensus.setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS",false));
+    showGroupConservation.setSelected(Cache.getDefault("SHOW_GROUP_CONSERVATION", false));
+    showConsensHistogram.setSelected(Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM",true));
+    showConsensProfile.setSelected(Cache.getDefault("SHOW_CONSENSUS_PROFILE",false));
+    
     padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
 
     /***************************************************************************
@@ -229,7 +229,7 @@ public class Preferences extends GPreferences
     usagestats.setSelected(Cache.getDefault("USAGESTATS", false));
     questionnaire.setSelected(Cache.getProperty("NOQUESTIONNAIRES")==null); // note antisense here
     versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true)); // default is true
-
+    annotations_actionPerformed(null); // update the display of the annotation settings
     try
     {
       jbInit();
@@ -281,6 +281,10 @@ public class Preferences extends GPreferences
     Cache.applicationProperties.setProperty("ID_ITALICS", Boolean
             .toString(idItalics.isSelected()));
     Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",Boolean.toString(showUnconserved.isSelected()));
+    Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS",Boolean.toString(showGroupConsensus.isSelected()));
+    Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",Boolean.toString(showGroupConservation.isSelected()));
+    Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM",Boolean.toString(showConsensHistogram.isSelected()));
+    Cache.applicationProperties.setProperty("SHOW_CONSENSUS_PROFILE",Boolean.toString(showConsensProfile.isSelected()));
     Cache.applicationProperties.setProperty("ANTI_ALIAS", Boolean
             .toString(smoothFont.isSelected()));
 
@@ -471,6 +475,10 @@ public class Preferences extends GPreferences
     conservation.setEnabled(annotations.isSelected());
     quality.setEnabled(annotations.isSelected());
     identity.setEnabled(annotations.isSelected());
+    showConsensHistogram.setEnabled(annotations.isSelected());
+    showConsensProfile.setEnabled(annotations.isSelected());
+    showGroupConsensus.setEnabled(annotations.isSelected());
+    showGroupConservation.setEnabled(annotations.isSelected());
   }
 
   public void newLink_actionPerformed(ActionEvent e)